ABSTRACT Unbalanced chromosome content, so-called aneuploidy, is a hallmark of many human genetic diseases and cancers. Aneuploidy not only results in the altered expression of the genes encoded on the aneuploid chromosome, but also affects gene expression genome-wide. For many aneuploidy related diseases, it is still not clear which gene or gene sets are the key drivers of disease pathology. Research on molecular consequences of aneuploidy could shed invaluable light on ?genotype-phenotype? association, thus leading to a better understanding of disease development mechanisms. Due to the known substantial post-transcriptional processes in aneuploidy condition and the functional importance of proteins, proteomic measurement is indispensable to identify genes that are dosage-imbalanced at the protein level. However, biological and technical challenges such as the variability of the individual genome, the limited quantitative reproducibility and accuracy of the measurement, and the lack of strategies for identifying indirect mechanisms have hindered efficient proteomic scrutiny on aneuploidy. We hypothesize that the aneuploid cells would employ characteristic proteostasis and cell signaling pathways to deal with the large-scale protein dosage imbalance, and that the newly acquired or altered protein-protein interactions under aneuploidy stress play an important role in regulating molecular network and cellular fitness. In this proposal, we will use isogenic cell models from human and mouse aneuploidy cases. We will further develop and apply the techniques based on quantitative mass spectrometry and new analytical strategies based on protein- context profiling to discover the direct and indirect proteomic effects in the aneuploidy models. Results from this proposal are extremely important. First, the proteomic- centric, multilayered dataset will describe how protein homeostasis is maintained when several hundreds of genes that are gained or lost, decipher commonly activated signaling processes across aneuploidy models, and provide opportunities to predict the cellular impact of specific gene copy number alteration (CNA). Second, the protein-context profiling technique will be an invaluable tool for identifying de novo protein functions and associations in aneuploidy and other disease conditions. Third, those significant proteins escaping the homeostasis control or tightly interacting to signaling hubs will provide a list of important protein targets for further functional studies in aneuploidy cases, such as lung squamous cell carcinomas and trisomy disorders that are relevant to the studied cell models.